Data from: History of expansion and anthropogenic collapse in a top marine predator of the Black Sea estimated from genetic data

Two major ecological transitions marked the history of the Black Sea after the last Ice Age. The first was the postglacial transition from a brackish-water to a marine ecosystem dominated by porpoises and dolphins, once this basin was reconnected back to the Mediterranean Sea (ca. 8,000 years B.P.). The second occurred during the last decades, when overfishing and hunting activities brought these predators close to extinction, deeply impacting the structure and dynamics of the ecosystem. Estimating the extent of this decimation is essential for characterizing this ecosystem's dynamics and for formulating restoration plans. However this extent is poorly documented in historical records. We addressed this issue for one of the main Black Sea predators, the harbor porpoise, using a population genetics approach. Analyzing its genetic diversity using an Approximate Bayesian Computation approach, we show that only a demographic expansion (at most 5,000 years ago) followed by a contemporaneous population collapse can explain the observed genetic data. We demonstrated that both the postglacial settlement of harbor porpoises in the Black Sea and the recent anthropogenic activities have left a clear footprint on their genetic diversity. Specifically, we inferred a strong population reduction (~90%) that occurred within the last five decades, which can therefore clearly be related to the recent massive killing of small cetaceans and to the continuing incidental catches in commercial fisheries. Our study thus provides a first quantitative assessment of these demographically catastrophic events, while also showing that two separate historical events can be inferred from contemporary genetic data.

末次冰期结束后，黑海的演化历程存在两大标志性生态转型事件。第一次为冰期后转型：当该海盆重新与地中海连通（距今约8000年）时，黑海从半咸水生态系统转变为以鼠海豚与海豚为主导的海洋生态系统。第二次转型发生在近数十年间：过度捕捞与捕猎活动致使这些捕食者濒临灭绝，深刻改变了该生态系统的结构与动态。精准估算此次种群锐减的规模，是解析该生态系统动态、制定生态修复计划的核心前提，但历史文献中对此的记载极为匮乏。为此，我们以黑海主要捕食物种之一的港湾鼠海豚（harbor porpoise）为研究对象，采用种群遗传学方法开展相关研究。通过近似贝叶斯计算（Approximate Bayesian Computation）方法分析其遗传多样性，我们发现：唯有当种群先经历一次距今至多5000年的种群扩张，随后发生同步的种群崩溃时，方能合理解释观测到的遗传数据。研究证实，黑海港湾鼠海豚的冰期后定居事件与近期人类活动，均在其遗传多样性层面留下了清晰的演化印记。具体而言，我们推断在过去五十年间，该种群出现了约90%的剧烈缩减，这一结果可直接归因于近期小型鲸类的大规模捕杀，以及商业渔业中持续存在的误捕问题。本研究首次对这两起具有种群统计学灾难性影响的事件开展了定量评估，同时证明可通过当代遗传数据推断出两次独立的历史事件。